EP0113673A2

EP0113673A2 - Signal processing method in autoradiography

Info

Publication number: EP0113673A2
Application number: EP84100145A
Authority: EP
Inventors: Hisashi Shiraishi; Tsutomu Kimura; Kazuhiro Hishinuma
Original assignee: Fuji Photo Film Co Ltd
Current assignee: Fujifilm Holdings Corp
Priority date: 1983-01-08
Filing date: 1984-01-09
Publication date: 1984-07-18
Also published as: US4888695A; EP0113673A3

Abstract

A signal processing method in autoradiography for determination of base sequence of DNA or DNA fragment, employing groups of radioactively labeled base specific cleavage products or mixture thereof obtained by specifically cleaving the DNA or DNA fragment labeled with a radioactive element and resolved one-dimensionally in parallel relation to each other to form resolved rows on a support medium, which comprises a process including:

(1) detecting sampling points in each resolved row;
(2) determining reference sampling points in each reference row which is practically provided on the support medium and/or synthesized from the resolved rows;
(3) joining the corresponding reference sampling points among said plural reference rows to fix plural continuous lines comprising straight lines, polygonal lines or curved lines; and
(4) comparing and identifying said sampling points in each resolved row utilizing said continuous lines;

said process being applied to a digital signal corresponding to an autoradiograph having the locational information on the groups of radioactively labeled cleavage products, said digital signal being obtained by utilizing a radiation image recording and reproducing method using a stimulable phospher sheet.

Description

BACKGROUND OF THE INVENTION

FIELD OF THE INVENTION

This invention relates to a signal processing method in autoradiography and more particularly, to a signal processing method of comparing and identifying the resolved positions of radioactively labeled substances in autoradiography for determination of base sequence of DNA.

DESCRIPTION OF THE PRIOR ART

Autoradiography has been known as a method for obtaining locational information on radioactively labeled substances distributed in at least one dimensional direction to form a row on a support medium.
For instance, the autoradiography comprises steps of: labeling organism-originating biopolymers such as proteins or nucleic acids with a radioactive element; resolving the radioactively labeled biopolymers, derivatives thereof, or cleavage products thereof (hereinafter referred to as radioactively labeled substances) on a gel support (support medium) through a resolving process such as electrophoresis to form a resolved pattern of the radioactively labeled substances (the resolved pattern is not visible); placing said support medium and a high-sensitivity type X-ray film together in layers for a certain period of time to expose the film and developing said film to give the autoradiograph of the resolved pattern as a visible image on the film; and obtaining the locational information of the radioactively labeled substances from said visible image. Further, the identification of the polymeric substances, determination of molecular weight of the polymeric substances and isolation of the polymeric substances are performed based on the obtained locational information.
The autoradiography has been effectively utilized for determining the base sequence of nucleic acids such as DNA (or DNA fragment, hereinafter "DNA" may be used to include DNA as well as DNA fragment) or the like.
Maxam-Gilbert method and Sanger-Coulson method are known as methods for sequencing DNA utilizing the autoradiography. In these methods, the base sequence of DNA is determined by geniously utilizing the characteristic structure of DNA that DNA is in the form of double helix structure consisting of two chain molecules, which are constituted by four constitutional base units, each unit having a base, namely adenine (A), guanine(G), thymine (T) or cytosine (C), and cross-linked by hydrogen bonding between the four bases, the hydrogen bonding between each constitutional base unit comprising only two combinations, namely G-C and A-T.
For instance, Maxam-Gilbert method is carried out as follows: A group containing a radioactive isotope of phosphorus (P) is attached to a chain molecule of DNA or a DNA fragment at one end to be sequenced to prepare a radioactively labeled DNA molecule, and then thus labeled DNA molecule is specifically cleaved at the constitutional base unit by a certain chemical reaction. This reaction is called a "base specific cleavage reaction". Then the obtained mixture of numerous cleavage products of the DNA or DNA fragment is resolved through gel electrophoresis to give resolved pattern of the numerous cleavage products (the pattern is not visible). An X-ray film is exposed to the resolved pattern and developed to obtain a visualized autoradiograph thereon, and the sequential position of each base from the radioiso- topically labeled end of the chain molecules is read by referring to the obtained autoradiograph and the applied base specific chemical reaction so as to determine the sequence of all bases in the aimed DNA.
In the conventional autoradiography utilizing the radiographic process, the visualization of the autoradiograph having the locational information on radioactively labeled substances on a radiographic film is essentially required.
Investigators analyzes the distribution of the radioactively labeled substances on a support medium through observation of the visualized autoradiograph. The sequence of DNA is determined by judging individual resolved positions of the radioactively labeled cleavage products (or mixture of cleavage products) of DNA on the visualized autoradiograph, and then comparing the resolved positions among the resolved rows thereof.
Since the conventional autoradiography requires the visual analysis of the autoradiograph, there is brought about a drawback that the locational information on the radioactively labeled substances obtained by analysis of the visualized autoradiograph varies or flucturates depending on the skill of investigators, and the accuracy of the information is limited to a certain extent. Particularly, in such cases that the autoradiograph visualized on a radiographic film shows an image of reduced quality (in regard of sharpness, contrast, etc.), the satisfactory information can be hardly obtained and the accuracy is low. In order to improve the accuracy of the locational information, for instance, a visualized autoradiograph has been scanned with a device such as a scanning densitometer. However, such scanning process requires increased operation time and complicated procedure. Further, there is a limitation on increase of the accuracy so far as such method merely using device is employed.
For instance, in carrying out the exposing procedure, the support medium carrying the above-mentioned resolved rows thereon and a radiographic film sometimes cannot be accurately arranged together in layers. In such case, the resolved rows (e.g., electrophoretic rows) visualized on the radiographic film are made to be not parallel to the longitudinal direction of the film to give a dislocated pattern. As a result, error is introduced into the visual analysis of the locational information on the radioactively labeled substances and to decrease the accuracy thereof.
Further, the rows of the resolved radioactively labeled substances on the support medium are sometimes made non-parallel to the longitudinal direction of the support medium or made distorted depending on nature of the support medium or resolving conditions. For instance, a gel support medium is generally held between two glass plates in the resolving procedure because the gel lacks self-supporting property. As a result, the gel occasionally becomes uneven in the thickness due to the deformation of the covers such as glass plates and accordingly the radioactively labeled substances are not always resolved uniformly on the gel. The lack of uniformity of the resolved pattern is also caused by air foams contained in the gel or by heterogenous dispersion of the composition of gel. For these reasons, a phenomenon such as the so-called smiling effect, i.e., a phenomenon that the migration distance of the resolved row in the vicinity of the center of the support medium is longer than those in the both sides thereof, is often observed. Additionally, if the voltage is not applied uniformly to the support medium in electrophoresis, the resolving conditions are made locally uneven on the support to destort the resolved rows.
There is known no suitable method but a method of manually correcting the distortion of resolved rows. Accordingly, it is not easy to analyze the locational information on the radioactively labeled substances in the above-described cases. Even if the aforementioned device is used, it is still difficult to obtain a satisfactorily accurate locational information on the radioactively labeled substances.

SUMMARY OF THE INVENTION

The present inventors have discovered that an autoradiograph having the information on one dimensional location of the radioactively labeled substances in a sample is obtained as digital signal without necessity of visualization thereof, by utilizing a radiation image recording and reproducing method using a stimulable phosphor sheet in place of the conventional radiography using a radiographic film. In the present method, the digital signal is subsequently subjected to an appropriate signal processing to determine the base sequence of DNA or DNA fragment with ease and high accuracy.
The present invention provides a signal processing method in autoradiography for determination of base sequence of DNA or DNA fragment, employing radioactively labeled cleavage products obtained by specifically cleaving the DNA or DNA fragment labeled with a radioactive element, comprising:

1) at least two sets of reference mixtures consisting essentially of guanine specific cleavage products, adenine specific cleavage products, thymine specific cleavage products and cytosine specific cleavage products; and
2) at least one group of cleavage products or mixture thereof containing at least one kind of the base specific cleavage products,
both 1) and 2) being resolved one-dimensionally in such parallel relation that resolved rows of said two sets of reference mixtures 1) sandwitch at least one resolved row of the group 2) to form at least three resolved rows on a support medium,

(1) detecting reference sampling points in each reference row, the reference row being the resolved row of-the reference mixture;
(2) detecting sampling points in the resolved row other than the reference rows;
(3) joining the corresponding reference sampling points among said plural reference rows to fix plural continuous lines comprising straight lines, polygonal lines or curved lines; and
(4) comparing and identifying said sampling points in the resolved row other than the reference rows utilizing said continuous lines;

The present invention also provides a signal processing method in autoradiography in which all the above sets of reference mixtures 1) of DNA or DNA fragment are replaced with sets of specimens for synthesizing a reference row, the set comprising at least two groups of cleavage products or mixture thereof and the groups being in such combination as to totally contain guanine specific cleavage products, adenine specific cleavage products, thymine specific cleavage products and cytosine specific cleavage products; and each reference row is synthesized from resolved rows of the specimen through the signal processing.
Further, the present invention provides a signal processing method which is in combination of the above-mentioned two methods, that is, using at least one set of the reference mixture and at least one set of the specimen for synthesizing a reference row, the reference rows for the signal processing consist essentially of the resolved row of the reference mixture and the synthesized row from resolved rows of the specimen.
In the present invention, the reference row means a row corresponding to a resolved row of a mixture of all the cleavage products consisting essentially of guanine specific cleavage products, adenine specific cleavage products, thymine specific cleavage products and cytosine specific cleavage products, and is employed as an internal reference for each resolved row of radioactively labeled base specific cleavage products in the signal processing for determination of the base sequence of DNA or DNA fragment.

BRIEF DESCRIPTION OF DRAWINGS

Figure 1 shows an example of the read-out system for reading out the locational information of the radioactively labeled substances copied from the sample and stored in a stimulable phosphor sheet employable in the present invention.
Figure 2 shows an example of the autoradiograph of resolved rows comprising base specific cleavage products of DNA.
Figure 3 shows a part of contour lines which are prepared from the reference sampling points and approximated with curved lines.

DETAILED DESCRIPTION OF THE INVENTION

The present invention utilizes the radiation image recording and reproducing method which comprises steps of: causing a stimulable phosphor of a stimulable phosphor sheet to absorb radiation energy having passed through an object or having been radiated by an object; exciting the stimulable phosphor with an electromagnetic wave such as visible light or infrared rays (hereinafter referred to as "stimulating rays") to sequentially release the radiation energy stored in the stimulable phosphor as light emission; and photoelectrically detecting the emitted light to give an electric signal; or further reproducing the electric signal in the form of a visible image on a recording material, or converting the electric signal to digital signal through A/D conversion.
Details of the above-mentioned radiation image recording and reproducing method is described in, for instance, U. S. Patent No. 4,239,968.
The stimulable phosphor sheet contains a stimulable phosphor such as a divalent europium activated alkaline earth metal fluorohalide phosphor. When exposed to a radiation such as X-rays, a-rays, B-rays, y-rays, or ultraviolet rays, the stimulable phosphor absorbs a portion of the radiation energy and then emits light (stimulated emission) corresponding to the radiation energy stored therein upon excitation with an electromagnetic wave (stimulating rays) such as visible light or infrared rays, after exposure.
Accordingly, the locational information on the radioactively labeled substances in the present invention can be directly obtained as digital signal through no visualization by applying the above-mentioned radiation image recording and reproducing method to the autoradiography.
In the present invention, the term "locational information" of the radioactively labeled substances (or products) means to include a variety of information relating to the location of the radioactively labeled substances, or the aggregation thereof, being present in the sample, such as the location, the shape, the concentration, the distribution, and combinations thereof.
According to the present invention, the base sequence of DNA or DNA fragment can be determined with high accuracy, even if there occurs the distortion or dislocation in the overall length of the autoradiograph stored in the stimulable phosphor sheet due to the locational distortion of resolved rows of the radioactively labeled substances on the support medium occurring in the course of the resolving procedure, or due to the locational distortion occurring between the support medium on which the resolved rows thereof are formed in one dimensional direction and the stimulable phosphor sheet in the course of the copying and storing` procedure of the autoradiograph. Particularly in the case that the distortion is observed in the resolving direction, the present invention makes possible to identify the resolved portions through determination of a level of the distortion on the degital image data with reference to a certain reference row and subsequent correction on respective resolved rows, by providing plural reference rows (internal references) in the signal processing. A portion or all of the plural reference rows can be obtained by providing resolved rows of the reference mixtures on the support medium and/or by synthesizing from resolved rows of the specimens for synthesizing a reference row. Thus, the base sequence of aimed DNA can be determined smoothly and with high accuracy. More in detail, reference sampling points in the reference row (internal reference) can be obtained with high accuracy in the case of using a set of the reference mixtures and providing the resolved row thereof on the support medium. On the other hand, in the case of using a set of specimen for synthesizing a reference row and synthesizing the reference row through the signal processing, the reference sampling points in the reference row can be obtained without unnecessary increase of the number of resolved rows on the support medium because the specimen also serves as a set of substances for determination.
Accordingly, it is possible to achieve the DNA sequencing not only with high accuracy due to the provision of precise reference row but also with the increased amount of information in one autoradiographic process, especially in the case of using the combination of the reference mixture and the specimen for synthesizing a reference row. When three or more of reference rows are utilized in the signal processing, the reference rows may be obtained in an optional combination of the reference mixture and the specimen for synthesizing a reference row.
Furthermore, it is possible to detect the resolved positions of the radioacitively labeled substances with high accuracy even if the area of the individual resolved portion thereof is small. This means that the absolute amount of the radioactively labeled substances used in one autoradiographic process can be reduced, otherwise that the number of resolved rows providable on a single support medium can increase without broadening the width of support medium to give more information than the case using the conventional autoradiographic process.
Examples of the sample employable in the present invention include a support medium on which base specific cleavage products and/or a mixture thereof, obtained ₃y base-specifically cleaving DNA or DNA fragment labeled with a radioactive element are resolved (or developed) in one dimensional direction to form resolved rows.
Representative examples of the method for resolving (or developing) the above-mentioned radioactively labeled substances on a support medium include an electrophoresis using one of various resolving medium such as a gel in the form of layer, column or the like, a molded polymer film such as a cellulose diacetate film, and a filter paper, and a thin layer chromatography using a support of material such as silica gel. Among these, the electrophoresis using a gel support medium is pre- ferrably employed in the present invention.
The stimulable phosphor sheet employable in the present invention has a basic structure comprising a support, a phosphor layer and a transparent protective film. The phosphor layer comprises a binder and a stimulable phosphor dispersed therein, and for instance, it can be obtained by dipersing particulate divalent europium activated barium fluoride (BaFBr:Eu2⁺) phosphor particles in a mixture of nitrocellulose and linear polyester. The stimulable phosphor sheet is, for example, prepared by providing the above-mentioned phosphor layer onto the support such as a polyethylene terephthalate sheet and then providing a protective film such as a polyethylene terephthalate sheet on the phosphor layer.
Details on the support medium and the stimulable phosphor sheet employable in the invention are described, for instance, in Japanese Patent Application No. 57(1982)-193419 (the content is given in U. S. Patent Application filed on November 7, 1983, and European Patent Application 83 110 984.8).
In carrying out the exposing procedure, that is, the procedure of storing the radiation energy released from the support medium containing the radioactively labeled substance in the stimulable phosphor sheet, at least a portion of the released radiation energy is absorbed in the stimulable phosphor sheet by placing the support medium and stimulable phosphor sheet together in layers for a certain period of time. The exposure can be accomplished by keeping the phosphor sheet in a position adjacent to the support medium, and for instance, at room temperature or lower temperature for at least several seconds.
Details of the exposing procedure employable in the invention are described in Japanese Patent Application No. 57(1982)-193418 (the content is given in U. S. Patent Application filed on November 7, 1983, and European Patent Application 83 110 984.8).
A method for reading out or detecting the information on one dimensional location of the radioactively labeled substances in the sample copied and stored in the stimulable phosphor sheet according to the invention will be described briefly, referring to an embodiment of a read-out system shown in Figure 1 of the accompanying drawings.
Figure 1 schematically illustrates an embodiment of the read-out system comprising a preliminary read-out section 2 for preliminarily reading out the one dimensional information on the location of the radioactively labeled substances stored (or recorded) in the stimulable phosphor sheet 1 (from which the sample generally has been removed, the stimulable phosphor sheet is hereinafter referred to as "phosphor sheet"), and a final read-out section 3 for finally reading out the desired locational information on the radioactively labeled substance stored in the phosphor sheet 1.
In the preliminary read-out section 2, the preliminary read-out operation is carried out in the following manner.
Laser beam 5 generated by a laser source 4 first passes through a filter 6 to cut off a light beam in the wavelength region corresponding to the wavelength region of stimulated emission to be emitted from the phosphor sheet 1 in response to stimulation with the laser beam 5. The laser beam 5 is subsequently deflected by a beam deflecter 7 such as a galvanometer mirror, and reflected by a plane reflecting mirror 8. The deflected beam then impinges upon the phosphor sheet 1. The laser source 4 used herein is so selected as to avoid overlapping of the wavelength region of the laser beam 5 with the main wavelength region of the stimulated emission to be emitted from the phosphor sheet 1.
The phosphor sheet 1 is transferred to the direction along the arrow 9 under the irradiation of the above-mentioned deflected laser beam. Therefore, the whole surface of the phosphor sheet 1 is subjected to the irradiation of the deflected laser beam. The power of the laser beam 5 employed in the preliminary read-out section is adjusted to be lower than the power of the laser beam to be employed in the final read-out section by controlling the output of the laser source 4, the beam diameter of the laser beam 5, the scanning speed of the laser beam 5, and the transferring speed of the phosphor sheet 1.
When irradiated with the above-mentioned laser beam, the phosphor sheet 1 gives the stimulated emission having the emission intensity proportional to the radiation energy stored (or recorded) therein. The emission then enters into a light guiding sheet 10 for the preliminary read-out. The light guiding sheet 10 has a linear edge face for receiving the emission, and the edge face is so positioned in the vicinity of the phosphor sheet as to correspond to the scanning line on the phosphor sheet 1. The exit of the light guiding sheet 10 is in the form of a ring and is connected to an light-receiving face of a light detector 11 such as a photomultiplier. The light guiding sheet 10 is made, for instance, by processing a sheet of a transparent thermoplastic resin such as an acrylic synthetic resin, and so constituted that the emission introduced from the linear edge face is transmitted to the exit under repeated total reflection within the sheet 10. The stimulated emission from the phosphor sheet 1 is guided in the interior of the light guiding sheet 10 to the exit, and received by the light detector 11.
The preferable shape and material of the light guiding sheet is disclosed in Japanese Patent Provisional Publications No. 55(1980)-87970 and No. 56(1981)-11397, etc.
On the light-receiving face of the light detector 11 is provided a filter which allows only the light of wavelength region of the stimulated emission to'pass through and cuts off the light of the wavelength region of the stimulating rays (laser beam) so as to detect only the stimulated emission. The stimulated emission detected by the light detector 11 is converted to an electric signal, amplified in an amplifier 12 and transmitted to the output. The stored information output from the amplifier 12 is supplied to a control circuit 13 of the final read-out section 3. The control circuit 13 provides an amplification degree setting value a and a scale factor setting value b in order to obtain a signal having a suitable level according to the detected information.
The phosphor sheet 1 having been subjected to the preliminary read-out in the above-described manner is then transferred to the final read-out section 3.
In the final read-out section 3, the following read-out operation is performed.
The laser beam 15 generated by a laser source 14 for the final read-out passes through a filter 16 having the same function as that of the above-mentioned filter 5, and then the beam diameter is precisely adjusted in a beam expander 17. Subsequently, the laser beam is ieflected by a beam deflector 18 such as a galvanometer nirror, and reflected by a plane reflection mirror 19. The deflected beam then impinges one-dimensionally upon the phosphor sheet 1. Between the beam deflector 18 and the plane reflection mirror 19 a fθ lens 20 is provided so that the beam speed is continuously kept constant when the deflected laser beam is scanned on the phosphor sheet 1.
The phosphor sheet 1 is transferred in the direction along the arrow 21 under the irradiation with the above-mentioned deflected laser beam. Accordingly, the whole surface of the phosphor sheet is subjected to the irradiation in the same manner as in the preliminary read-out operation.
When irradiated with the above-mentioned laser beam, the phosphor sheet 1 gives the stimulated emission in proportion to the radiation energy stored therein in the same manner as in the preliminary read-out operation. The emission then enters into a light guiding sheet 22 for the final read-out. The light guiding sheet 22 for the final read-out is of the same material and has the same constitution as the light guiding sheet 10 employed for the preliminary read-out. The stimulated emission received is guided in the interior of the light guiding sheet 22 up to the exit under repeated total reflection, and then received by a light detector 23. On the light-receiving face of the light detector 23 is provided a filter which allows only the light of wavelength region of the stimulated emission to pass through and cuts off the light of the wavelength region of the stimulating rays (laser beam) so as to detect only the stimulated emission. The stimulated emission detected by the light detector 23 is converted to an electric signal, amplified to an electric signal adjusted to an appropriate level in an amplifier 24 according to the aforementioned amplification degree setting value a and transmitted to an A/D converter 25. The adjusted electric signal is then converted to a digital signal in the A/D converter 25 according to an appropriate scale facter defined by the scale factor setting value b.
In the above descripiton on the method for reading out the locational information on the radioactively labeled substances copied and stored in the stimulable phosphor sheet, a read-out operation involving both the preliminary read-out operation and the final read-out operation has been given. However, the read-out operation employable in the present invention is not limited to the above-described embodiment. For instance, the preliminary read-out operation may be omitted if the content of the radioactive substances in the sample and an adequate exposure time for the sample is previously known.
Further, other suitable methods than the above-mentioned embodiments may be used for reading out the locational information of the radioactively labeled substances copied from the sample and stored in the stimulable phosphor sheet.
Thus obtained digital signal corresponding to the autoradiograph of the sample is subsequently input into the signal processing circuit 26. In the signal processing circuit 26, the information on one dimensional location of the radioactively labeled substances is processed by the signal processing and represented with symbols and/or numeral so as to determine the sequence of aimed DNA.
The signal processing method of the present invention for the determination of base sequence of DNA is described below, utilizing the above-mentioned Maxam-Gilbert method and referring to an example using the combination of the reference mixture containing all the base specific cleavage products and the specimen for synthesizing a reference row consisting of two groups and containing all the base specific cleavage products as a whole. The example comprises the following five groups of base specific cleavage products for different three kinds of DNA resolved on a support medium through the electrophoresis, which are a typical combination of cleavage product groups:

1) guanine (G) specific cleavage products
+ adenine (A) specific cleavage products
- + thymine (T) specific cleavage products
- + cytosine (C) specific cleavage products,
2) guanine (G) specific cleavage products
- + adenine (A) specific cleavage products,
3) thymine (T) specific cleavage products
- + cytosine (C) specific cleavage products,
4) guanine (G) specific cleavage products,
5) cytosine (C) specific cleavage products.

The three kinds of DNA labeled with a radioactive element ( 32 P) are specifically cleaved at the constitutional base units according to the conventional manner respectively to prepare three sets of the above groups 1) to 5) of base specific cleavage products. However, it is enough to prepare at least one set of the reference mixture 1) in this combination. The prepared three sets of the five groups of radioactively labeled cleavage products are respectively resolved on a gel support medium through electrophoresis to obtain a sample, which is performed in such a manner that a resolved row of the reference mixture 1) and two resolved rows of the two groups 2) and 3) consisting essentially of the mixture of cleavage products (namely, a set of specimen for synthesizing a reference row) sandwitch resolved rows of at least the two groups 4) and 5) of base specific cleavage products.
Then, the sample (support medium on which the resolved rows are formed) is placed on a stimulable phosphor sheet together in layers at room temperature for several minutes to perform the exposure, and the autoradiograph of the sample is recorded and stored in the stimulable phosphor sheet.
Figure 2 shows an autoradiograph of resolved rows (electrophretic rows) comprising the above-mentioned five groups of the radioactively labeled cleavage products for three kinds of DNA. That is, the first to thirteenth rows (electrophoretic rows) shown in Figure 2 in order correspond to,

(1) - (G) specific cleavage products
- + (A) specific cleavage products,
(2) - (T) specific cleavage products
- + (C) specific cleavage products,
(3) - (G) specific cleavage products,
(4) - (C) specific cleavage products,
(5) - (G) specific cleavage products,
(6) - (G) specific cleavage products
- + (A) specific cleavage products,
(7) - (G) specific cleavage products
- + (A) specific cleavage products
- + (T) specific cleavage products
- + (C) specific cleavage products,
(8) - (T) specific cleavage products
- + (C) specific cleavage products,
(9) - (C) specific cleavage products,
(10) - (G) specific cleavage products,
(11) - (C) specific cleavage products,
(12) - (G) specific cleavage products
- + (A) specific cleavage products, and
(13) - (T) specific cleavage products
+ (C) specific cleavage products.

The 1st to 4rh rows, the 5th to 9th rows, and the 10th to 13th rows are groups of resolved rows of different DNA, respectively. The 7th row is of the reference mixture; and the 1st & 2nd rows and the 12th & 13th rows are of the specimens for synthesizing a reference row, respectively.
The digital signal obtained by reading out the autoradiograph recorded and stored in the stimulable phosphor sheet by means of the read-out system shown in Figure 1 is provided with an address (X, Y) which is represented by a coordinate system fixed to the stimulable phosphor sheet and with a level of signal (Z) in its address which corresponds to the intensity of stimulated emission. That is, the obtained digital signal corresponds to the autoradiograph shown in Figure 2 and digital image data having the locational information on the above-mentioned radioactively labeled substances are input into the signal processing circuit 26. In the present invention, the digital image data mean a set of the digital signals corresponding to the autoradiograph of the radioactively labeled substances.
In the first place, resolved positions of the radioactively labeled substances are detected on the above-mentioned 13 rows on the digital image data, and the detected resolved positions are assigned to sampling points. For example, the sampling points are detected as follows.
The digital image data are scanned at two different positions in parallel and in such a manner that the scanning traverses the one-dimensionally distributed (resolved) row of the radioacitively labeled substances to detect distribution points thereof in each row on each scanning (this scanning for detecting the distribution points is referred to as preliminary scanning); and the two distribution points for each row are joined to give thirteen straight lines, and the straight lines are assigned to scanning lines for detecting the sampling points in each resolved row.
In the signal processing method of the present invention, the obtained digital signal is temporarily stored in a memory device of the signal processing circuit 26 (that is, a non-volatile memory unit such as a buffer memory, a magnetic disk, etc.). In the signal processing, the scanning on the digital image data means to selectively pick up only the signal in the scanning area from the memory device.
Then, the scanning with the scanning line for detecting sampling points is performed on the digital image data to obtain a function f(W) which represents the signal level on the scanning area, wherein W represents the position on the scanning line. The smoothing is applied to the function f(W) through convolution with a suitable filter function and the like, to obtain a function g(W). Subsequently the threshold-processing is applied to the function g(W). That is, the function g(W) is converted into a continuous function having only 1 and 0 by the operation:

wherein a₀ is a threshold value.
All middle points of regions of g(W) = 1 in the function g(W) are assigned to sampling points. The threshold value (a_o) employed in the threshold processing can be determined, for instance, based on a relationship between the signal level and the frequency thereof with respect to the digital signal in the scanning area, namely a histogram.
Thus, a set of the sampling points {S_kn (X_kn, Ykn, Z_kn)} can be detected for each row, wherein k is a positive integer and represents the number of row; and n is a positive integer and represents the number of sampling point. The sampling point S _kn means the n-th sampling point in the k-th row. The process for detecting the sampling points is by no means restricted to the above-described process.
In the second place, by performing a logical sum operation between the sampling points in the first row and the sampling points in the second row, a row composed of sampling points for all the four base specific cleavage products which consist essentially of (G) specific cleavage products, (A) specific cleavage products, (T) specific cleavage products and (C) specific cleavage products, namely a reference row (internal reference row) of {S_14n} is newly obtained. This synthesis is, for instance, represented by the following operation:
wherein it represents a set of sampling points and U represents a logical sum operator. The reference sampl- in^{g point {}S_14n} is fixed at such a new coordinate that the synthesized reference row imaginarily exist between the first row and second row.
A reference row having reference sampling points S_15n} is synthetically obtained by the above-mentioned operation between the sampling points in the twelfth row and the sampling points in the thirteenth row, and sampling points of the eleventh row and twelfth row respectively.
The seventh row is a resolved row of the reference mixture (i.e., reference row) and the sampling points thereof are reference sampling points. Accordingly, there are provided three reference rows (containing the imaginary reference rows) on the digital image data; one in the center and two in the both sides of the thirteen electrophoretic rows obtained by resolution.
In the third place, a plurality of straight lines (or polygonal lines) are obtained by joining the corresponding reference sampling points in each reference row, or reference sampling points having the same sampling point number n. For instance, the reference sampling points S_14,1', S_7,1 and S_15,1 at the farthest resolved positions (n = 1) are joined to obtain a polygonal line, and the other reference sampling points (n = 2, 3, ...) are subsequently joined in the same manner as mentioned above to obtain straight lines (or polygonal lines) as same as the minimum number of reference sampling points in a reference row. The polygonal lines may be further approximated by a suitable curve. Thus obtained continuous lines comprising straight lines, polygonal lines, and/or curved lines can be considered to be a series of contour lines {Ln}, wherein n coincides with the reference sampling point number n.
Figure 3 shows a part of the contour lines approximated by curves as mentioned above.
In the next place, the sampling points in the other rows than the reference rows are compared and identified with reference to the contour lines. For instance. concerning the sampling point S_3,1 in the third row, it is judged which of the contour line L₁ or L₂ the sampling point S_3,1 is positioned nearer to, and if the nearer contour line is L₁, the sampling point S3,1 is assigned to the reference sampling point S_{14 ,1}. All the sampling points in the third row are subsequently assigned to any one of the reference sampling points in the same manner as mentioned above. In summary, the sampling points in the third row are represented by a subset {S_14n}₃ of the reference sampling points or a subset {L_n}₃ of the contour lines.
Thus the sampling point S_kn represented by the X-Y coordinate (X_kn' Y_kn) can be also represented by the contour line L_n. Since the series of contour lines can n be assumed to be the electrophoretic coordinate, the above-mentioned process can be regarded, in other words, to be the coordinate transformation from the X-Y coordinate to the electrophoretic coordinate L .
A set of sampling points in the third row which are assigned to the reference sampling points is included in a set of sampling points in the first row constituting the reference row, and consequently the imaginary sixteenth row having a new set {S_16,n} of sampling points is obtained by the logical product opearation.
The obtained sixteenth row corresponds to a resolved row of adenine specific cleavage products in the groups of the first through fourth rows.
The same operation is performed between the fourth row and the second row to obtain the seventeenth row corresponding to a resolved row of thymine specific cleavage products. Then, concerning the third, fourth, sixteenth and seventeenth rows, the reference sampling point S_14n is compared with the sampling point S_kn in an increasing order of n, and when the former coincides with the latter, the reference sampling point S_14n is replaced with the coincident sampling point S_kn. To arrange the reference sampling points in the reference row in an increasing order of n, for instance, the following arrangement can be obtained.
Into the above _arrang_ment, _{S3n = G}, S_4n= C, S_16n = A and S_17n = T are introduced to give the following scheme.
Thus, the base sequence of one chain molecule of DNA which has been resolved in the groups of the first through fourth rows is determined.
The same processing is carried out for the fifth through ninth rows and the tenth through thirteenth rows to determine the sequences of one chain molecules of two kinds of DNA respectively.
The representation mode of the information on the base sequence of DNA obtained as described hereinbefore is by no means limited to the above-mentioned representation mode, and other representation modes may be utilized optionally. For instance, the relative amount of resolved base specific cleavage products can be also obtained to represent by processing the signal level on the scanning line with an optional operation, if desired.
Further, the base sequence of both two chain molecules of DNA can be represented. That is, by giving the information on the combination between the four bases, namely A-T and G-C, the sequence of DNA is represented by the following scheme.
The method for determining the base sequence of DNA utilizing the aforementioned combinations of (G+A, T+C, G, C, G+A+T+C) is an example of the determination of the sequence of DNA, and the signal processing of the present invention is by no means limited to the above combination, but various combinations are employable to determine the sequence of DNA in the same manner as described above.
Whatever combination is utilized, however, the combination is required to have the reference mixtures containing all the base specific cleavage products (G + A + T + C) and/or the specimens for synthesizing a reference row totally containing thereof (G, A, T, C). Additionally, it is required that two or more of resolved rows of a set of the specimen for synthesizing a reference row are provided adjacent to each other on the support medium, and that sets of resolved rows for obtaining reference rows (containing a resolved row of the reference mixture) are so provided as to sandwitch resolved rows of base specific cleavage products to be sequenced.
The above description is naturally applicable to the cases that all reference rows are provided by the reference mixture, and that all reference rows are provided by synthesis, as well as the case that the reference rows are provided by both the reference mixture and synthesis.
The sets of resolved rows of the mixtures and/or the specimens for synthesizing a reference row are preferably provided apart each other as far as possible in order to determine the base sequence of DNA with high accuracy. More in detail, these sets are preferably provided in the both side ends of plural resolved rows in the case of two sets, and the sets are preferably provided in the both side ends and in the center thereof in the case of three sets. In the case that more than three sets are involved, these sets are preferably provided independently between resolved rows aimed to sequence, with a suitable interval. The provision of three or more of sets of resolved rows for obtaining a reference row are effective to determine the sequence of DNA especially when the aformentioned smiling effect is observed on the support medium on which the radioactively labeled substances are resolved. By increasing the number of sets of resolved rows for obtaining a reference row on the support medium, the contour lines obtained by using the reference rows are more precise and the base sequence of DNA can be determined with higher accuracy.
In the case of using the reference mixture, the obtained reference row is more exact than in the case of employing an imaginary reference row obtained by synthesis, because the reference mixture is resolved simultaneously as one row on the support medium, so as to increase the precision of contour lines.
On the other hand, resolved rows of the specimen for synthesizing a reference row not only are employed to synthesize the reference row, but also serve per se as resolved rows to be sequenced respectively. Therefore, the more the number of resolved rows provided on the support medium is, the more the reference rows can be synthesized so as to obtain the more precise contour lines. Thus, the base sequence can be determined more accurately.
In the above-mentioned example, the present invention is described referring to the thirteen rows of the groups of radioactively labeled cleavage products resolved respectively in one dimensional directions on the support medium, but the resolved rows are by no means restricted to thirteen.
The information on the base sequence of DNA determined through the above-mentioned signal processing is output from the signal processing circuit 26, and subsequently transmitted to a recording device (not shown), directly or optionally via storage in a storing means such as a magnetic tape.
Various recording devices based on various systems can be employed for the above-described purpose, for instance, a device for visualizing optically by scanning on a photosensitive material with laser beam, etc., a display means for visualizing electrically on CRT, etc., a means for printing a radiation image displayed on CRT by mean of a video printer, and a means for visualizing on heatsensitive recording material using thermic rays.
It is further possible to perform the genetic philological information processing such as comparison between the obtained base sequence of the DNA and the base sequence of another DNA which has been already recorded and stored in a suitable place.

Claims

1. A signal processing method in autoradiography for determination of base sequence of DNA or DNA fragment, employing radioactively labeled cleavage products obtained by specifically cleaving the DNA or DNA fragment labeled with a radioactive element, comprising:

1) at least two sets of reference mixtures consisting essentially of guanine specific cleavage products, adenine specific cleavage products, thymine specific cleavage products and cytosine specific cleavage products; and

2) at least one group of cleavage products or mixture thereof containing at least one kind of the base specific cleavage products,

both 1) and 2) being resolved one-dimensionally in such parallel relation that resolved rows of said two sets of reference mixtures 1) sandwitch at least one resolved row of the group 2) to form at least three resolved rows on a support medium,
which comprises a process including:

(1) detecting reference sampling points in each reference row, the reference row being the resolved row of the reference mixture;

(2) detecting sampling points in the resolved row other than the reference rows;

(3) joining the corresponding reference sampling points among said plural reference rows to fix plural continuous lines comprising straight lines, polygonal lines or curved lines; and

(4) comparing and identifying said sampling points in the resolved row other than the reference rows utilizing said continuous lines;

said process being applied to a digital signal corresponding to an autoradiograph having the locational information on groups of the radioactively labeled cleavage products, said digital signal being obtained by causing a stimulable phosphor sheet to absorb radiation energy emitted by said groups of radioactively labeled cleavage products on the support medium to record the autoradiograph of the groups of radioactively labeled cleavage products on the stimulable phosphor sheet, scanning said stimulable phosphor sheet with an electromagnetic wave to release at least a portion of radiation energy stored in said phosphor sheet in the form of the autoradiograph as stimulated emission, and detecting said stimulated emission photoelectrically.

2. The signal processing method in autoradiography as claimed in claim 1, wherein at least three resolved rows of the reference mixtures 1) are so provided on the support medium that two resolved rows of the reference mixtures in close relation to each other sandwitch at least one resolved row of the group 2).

3. The signal processing method in autoradiography as claimed in claim 1 or 2, wherein the sampling points are detected by processing the digital signal on each scanning line for the plural resolved rows respectively with at least one processing selected from the group consisting of smoothing and threshold-processing.

4. The signal processing method in autoradiography as claimed in claim 1 or 2, wherein the employed cleavage products of DNA or DNA fragment comprise at least five groups including:

1) guanine specific cleavage products

+ adenine specific cleavage products

+ thymine specific cleavage products

+ cytosine specific cleavage products;

2) base specific cleavage products containing guanine specific cleavage products;

3) base specific cleavage products containing adenine specific cleavage products;

4) base specific cleavage products containing thymine specific cleavage products; and

5) base specific cleavage products containing cytosine specific cleavage products.

5. A signal processing method in autoradiography for determination of base sequence of DNA or DNA fragment, employing radioactively labeled cleavage products obtained by specifically cleaving the DNA or DNA fragment labeled with a radioactive element, comprising:

1) at least two sets of specimens for synthesizing a reference row, the set comprising at least two groups of cleavage products or mixture thereof, the groups being in such combination as to totally contain guanine specific cleavage products, adenine specific cleavage products, thymine specific cleavage products and cytosine specific cleavage products; and

both 1) and 2) being resolved one-dimensionally in such parallel relation that resolved rows of said two sets of specimens for synthesizing a reference row 1) which respectively comprise two or more rows sandwitch at least one resolved row of the group 2) to form at least five resolved rows on a support medium,
which comprises a process including:

(1) detecting sampling points in each resolved row;

(2) synthesizing a reference row from the two or more of resolved rows of the specimen with respect to each set of specimen and determining reference sampling points;

(4) comparing and identifying said sampling points in each resolved row utilizing said continuous lines;

said process being applied to a digital signal corresponding to an autoradiograph having the locational information on groups of radioactively labeled cleavage products, said digital signal being obtained by causing a stimulable phosphor sheet to absorb radiation energy emitted by said groups of radioactively labeled cleavage products on the support medium to record the autoradiograph of the groups of radioactively labeled cleavage products on the stimulable phosphor sheet, scanning said stimulable phosphor sheet with an electromagnetic wave to release at least a portion of radiation energy stored in said phosphor sheet in the form of the autoradiograph as stimulated emission, and detecting said stimulated emission photoelectrically.

6. The signal processing method in autoradiography as claimed in claim 5, wherein resolved rows of at least three sets of the specimens for synthesizing a reference row 1) which respectively comprise two or more rows are so provided on the support medium that said resolved rows of the two sets of the specimens in close relation to. each other sandwitch at least one resolved row of the group 2).

7. The signal processing method in autoradiography as claimed in claim 5 or 6, wherein the sampling points are detected by processing the digital signal on each scanning line for the plural resolved rows respectively with at least one processing selected from the group consisting of smoothing and threshold-processing.

8. The signal processing method in autoradiography as claimed in claim 5 or 6, wherein the set of specimen for synthesizing a reference row consists essentially of two groups of mixtures of base specific cleavage products including:

1) guanine specific cleavage products

+ adenine specific cleavage products; and

2) thymine specific cleavage products

+ cytosine specific cleavage products.

9. A signal processing method in autoradiography for determination of base sequence of DNA or DNA fragment, employing radioactively labeled cleavage products obtained by specifically cleaving the DNA or DNA fragment labeled with a radioactive element, comprising:

1) at least one set of a reference mixture consisting essentially of guanine specific cleavage products, adenine specific cleavage products, thymine specific cleavage products and cytosine specific cleavage products;

2) at least one set of specimen for synthesizing a reference row, the set comprising at least two groups of cleavage products or mixture thereof, the groups being in such combination as to totally include guanine specific cleavage products, adenine specific cleavage products, thymine specific cleavage products and cytosine specific cleavage products; and

3) at least one group of cleavage products or mixture thereof containing at least one kind of the base specific cleavage products,

these 1), 2) and 2) being resolved one-dimensionally in such parallel relation that a resolved row of the reference mixture 1) and two or more of resolved rows of the specimen for synthesizing a reference row 2) sandwitch at least one resolved row of the group 3) to form at least four resolved rows on a support medium,
which comprises a process including:

(1) detecting sampling points in each resolved row;

(2) assigning both the sampling points in a reference row being the resolved row of the reference mixture, and the sampling points in a reference row synthesized from the two or more of resolved rows of the specimen to reference sampling points;

10. The signal processing method in autoradiography as claimed in claim 9, wherein at least three sets of resolved rows in combination of a resolved row of the reference mixture 1) and two or more of resolved rows of the specimen for synthesizing a reference row 2) are so provided on the support medium that said two sets of resolved rows in close relation to each other sandwitch at least one resolved row of the group 3).

11. The signal processing method in autoradiography as claimed in claim 9 or 10, wherein the sampling points are detected by processing the digital signal on each scanning line for the plural resolved rows respectively with a at least one processing selected from smoothing and threshold-processing.

12. The signal processing method in autoradiography as claimed in claim 9 or 10, wherein the set of specimen for synthesizing a reference row 2) consists essentially of two groups of mixtures of base specific cleavage products including:

1) guanine specific cleavage products

+ adenine specific cleavage products; and

2) thymine specific cleavage products

+ cytosine specific cleavage products.